Sanku M wrote:
Hi,
I was planning to use Thermodynamic integration to calculate solvation
free energy of a molecule in a solvent. I was following Justin Lemkul's
online tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
. I found that
a) a sd integrator is used in stead of usual md integrator (
Leap-Frog integrator). I was wondering whether is it a specific
recommendation for thermodynamic integration to use stochastic integrator ?
It's simply a more accurate integrator for sensitive quantities for which
solvent viscosity may be important. It also controls temperature via the
Langevin method, which produces a proper canonical ensemble.
b) I also found DispCorr = EnerPres was also used to Apply long range
dispersion corrections for Energy and Pressure . Is it also a
recommendation to use with thermodyanmic integration technique ?
Dispersion correction is necessary when plain cutoffs are employed for
quantities that are sensitive to such truncation artifacts.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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